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Aliases for CLRN1 Gene

Aliases for CLRN1 Gene

  • Clarin 1 2 3 5
  • Usher Syndrome Type-3 Protein 3 4
  • USH3A 3 4
  • Usher Syndrome 3A 2
  • Clarin-1 3
  • RP61 3
  • USH3 3

External Ids for CLRN1 Gene

Previous HGNC Symbols for CLRN1 Gene

  • USH3
  • USH3A
  • RP61

Previous GeneCards Identifiers for CLRN1 Gene

  • GC03M152127
  • GC03M150643
  • GC03M148017

Summaries for CLRN1 Gene

Entrez Gene Summary for CLRN1 Gene

  • This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIIa. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLRN1 Gene

CLRN1 (Clarin 1) is a Protein Coding gene. Diseases associated with CLRN1 include Usher Syndrome, Type 3A and Retinitis Pigmentosa 61. An important paralog of this gene is CLRN2.

UniProtKB/Swiss-Prot for CLRN1 Gene

  • May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and presumably also in analogous synapses within the retina.

Gene Wiki entry for CLRN1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLRN1 Gene

Genomics for CLRN1 Gene

Regulatory Elements for CLRN1 Gene

Enhancers for CLRN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F150996 0.3 FANTOM5 26.3 -23.4 -23421 0.0 CLRN1 CLRN1-AS1 MED12L ENSG00000276055
GH03F151002 0.5 ENCODE 11.1 -30.2 -30155 1.7 ELF3 TBL1XR1 RAD21 YY1 ZNF143 FOS DEK MIXL1 ZNF654 CEBPB MED12L CLRN1 EIF2A CLRN1-AS1 SIAH2-AS1 ENSG00000243273 FAM188B2 ENSG00000276055
GH03F150925 1.5 FANTOM5 Ensembl ENCODE 11.1 +47.1 47120 1.0 CTCF ZNF654 PKNOX1 RNF2 REST RAD21 CBX8 GATA2 SMC3 KLF13 FAM188B2 ENSG00000243273 CLRN1 CLRN1-AS1 MED12L P2RY14 ENSG00000260234 ENSG00000244382
GH03F151012 1.3 Ensembl ENCODE 10.9 -41.8 -41849 3.9 HDGF PKNOX1 ATF1 ARNT SIN3A ARID4B DMAP1 SLC30A9 GATA2 NFYC CLRN1 CLRN1-AS1 MED12L ENSG00000276055
GH03F150876 0.4 Ensembl 10.6 +96.5 96520 0.2 CLRN1-AS1 CLRN1 ENSG00000243273
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around CLRN1 on UCSC Golden Path with GeneCards custom track

Genomic Location for CLRN1 Gene

150,918,911 bp from pter
150,973,020 bp from pter
54,110 bases
Minus strand

Genomic View for CLRN1 Gene

Genes around CLRN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLRN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLRN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLRN1 Gene

Proteins for CLRN1 Gene

  • Protein details for CLRN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • D3DNJ3
    • E1ACU9
    • Q8N6A9

    Protein attributes for CLRN1 Gene

    232 amino acids
    Molecular mass:
    25719 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CLRN1 Gene


neXtProt entry for CLRN1 Gene

Post-translational modifications for CLRN1 Gene

  • Glycosylation at Asn 48
  • Modification sites at PhosphoSitePlus

Other Protein References for CLRN1 Gene

No data available for DME Specific Peptides for CLRN1 Gene

Domains & Families for CLRN1 Gene

Protein Domains for CLRN1 Gene


Graphical View of Domain Structure for InterPro Entry



  • Belongs to the clarin family.
  • Belongs to the clarin family.
genes like me logo Genes that share domains with CLRN1: view

No data available for Gene Families for CLRN1 Gene

Function for CLRN1 Gene

Molecular function for CLRN1 Gene

UniProtKB/Swiss-Prot Function:
May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and presumably also in analogous synapses within the retina.
genes like me logo Genes that share phenotypes with CLRN1: view

Human Phenotype Ontology for CLRN1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CLRN1 Gene

MGI Knock Outs for CLRN1:

Animal Model Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , miRNA , Transcription Factor Targets and HOMER Transcription for CLRN1 Gene

Localization for CLRN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLRN1 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

Jensen Localization Image for CLRN1 Gene COMPARTMENTS Subcellular localization image for CLRN1 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 3
golgi apparatus 2
extracellular 1

Gene Ontology (GO) - Cellular Components for CLRN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IDA 19423712
GO:0005902 microvillus IDA 19423712
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030027 lamellipodium IDA 19423712
genes like me logo Genes that share ontologies with CLRN1: view

Pathways & Interactions for CLRN1 Gene

SuperPathways for CLRN1 Gene

No Data Available

Interacting Proteins for CLRN1 Gene

Gene Ontology (GO) - Biological Process for CLRN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007015 actin filament organization IDA 19423712
GO:0007601 visual perception IEA --
GO:0007605 sensory perception of sound IMP 15650299
GO:0010592 positive regulation of lamellipodium assembly IDA 19423712
GO:0045494 photoreceptor cell maintenance IMP 15521980
genes like me logo Genes that share ontologies with CLRN1: view

No data available for Pathways by source and SIGNOR curated interactions for CLRN1 Gene

Transcripts for CLRN1 Gene

mRNA/cDNA for CLRN1 Gene

Unigene Clusters for CLRN1 Gene

Clarin 1:
Representative Sequences:

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLRN1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6
SP1: - - -
SP2: - - - -
SP4: - -
SP5: - - -

Relevant External Links for CLRN1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLRN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLRN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLRN1 Gene

This gene is overexpressed in Adrenal Gland (x37.6).

NURSA nuclear receptor signaling pathways regulating expression of CLRN1 Gene:


SOURCE GeneReport for Unigene cluster for CLRN1 Gene:


mRNA Expression by UniProt/SwissProt for CLRN1 Gene:

Tissue specificity: Widely expressed. Found in the retina.
genes like me logo Genes that share expression patterns with CLRN1: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for CLRN1 Gene

Orthologs for CLRN1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLRN1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLRN1 34 35
  • 98.78 (n)
(Bos Taurus)
Mammalia CLRN1 34
  • 90.23 (n)
(Canis familiaris)
Mammalia CLRN1 34
  • 88.51 (n)
(Rattus norvegicus)
Mammalia Clrn1 34
  • 86.21 (n)
(Mus musculus)
Mammalia Clrn1 34 16
  • 85.92 (n)
(Monodelphis domestica)
Mammalia -- 35
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 78 (a)
(Gallus gallus)
Aves -- 35
  • 71 (a)
CLRN1 34
  • 70.34 (n)
(Anolis carolinensis)
Reptilia -- 35
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clrn1 34
  • 70.83 (n)
(Danio rerio)
Actinopterygii clrn1 34 35
  • 63.79 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4175 34
Species where no ortholog for CLRN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLRN1 Gene

Gene Tree for CLRN1 (if available)
Gene Tree for CLRN1 (if available)

Paralogs for CLRN1 Gene

Paralogs for CLRN1 Gene

(1) SIMAP similar genes for CLRN1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with CLRN1: view

Variants for CLRN1 Gene

Sequence variations from dbSNP and Humsavar for CLRN1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs111033258 Usher syndrome 3A (USH3A) [MIM:276902], Pathogenic 150,972,565(-) GTCAA(G/T)GCCTC nc-transcript-variant, upstream-variant-2KB, reference, missense
rs121908141 Usher syndrome 3A (USH3A) [MIM:276902], Pathogenic 150,941,656(-) CTTCA(A/C/T)GTACA nc-transcript-variant, reference, synonymous-codon, missense
rs121908142 Usher syndrome 3A (USH3A) [MIM:276902], Pathogenic 150,928,186(-) CTGTC(C/T)TGTCA nc-transcript-variant, reference, missense, utr-variant-3-prime
rs121908143 Usher syndrome 3A (USH3A) [MIM:276902], Pathogenic 150,972,591(-) TCCTC(G/T)GCAAA nc-transcript-variant, upstream-variant-2KB, reference, missense
rs374390376 Retinitis pigmentosa 61 (RP61) [MIM:614180], Pathogenic 150,972,617(+) ACAAC(A/C/G)GTGTC nc-transcript-variant, upstream-variant-2KB, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for CLRN1 Gene

Variant ID Type Subtype PubMed ID
esv275573 CNV gain+loss 21479260

Variation tolerance for CLRN1 Gene

Residual Variation Intolerance Score: 26.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.68; 14.41% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLRN1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLRN1 Gene

Disorders for CLRN1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for CLRN1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
usher syndrome, type 3a
  • usher syndrome type 3
retinitis pigmentosa 61
  • rp61
clrn1-related retinitis pigmentosa
usher syndrome
  • retinitis pigmentosa-deafness syndrome
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search CLRN1 in MalaCards View complete list of genes associated with diseases


  • Retinitis pigmentosa 61 (RP61) [MIM:614180]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:21310491}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Usher syndrome 3A (USH3A) [MIM:276902]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH3 is characterized by postlingual, progressive hearing loss, variable vestibular dysfunction, and onset of retinitis pigmentosa symptoms, including nyctalopia, constriction of the visual fields, and loss of central visual acuity, usually by the second decade of life. {ECO:0000269 PubMed:11524702, ECO:0000269 PubMed:12080385, ECO:0000269 PubMed:12145752, ECO:0000269 PubMed:15521980, ECO:0000269 PubMed:18273898, ECO:0000269 PubMed:23304067}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CLRN1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CLRN1: view

No data available for Genatlas for CLRN1 Gene

Publications for CLRN1 Gene

  1. Mutation screening of USH3 gene (clarin-1) in Spanish patients with Usher syndrome: low prevalence and phenotypic variability. (PMID: 15521980) Aller E. … Millan J.M. (Clin. Genet. 2004) 3 4 22 64
  2. Usher syndrome type III: revised genomic structure of the USH3 gene and identification of novel mutations. (PMID: 12145752) Fields R.R. … Sumegi J. (Am. J. Hum. Genet. 2002) 3 4 22 64
  3. Two novel disease-causing mutations in the CLRN1 gene in patients with Usher syndrome type 3. (PMID: 23304067) GarcA-a-GarcA-a G. … MillA!n J.M. (Mol. Vis. 2012) 3 4 64
  4. Alternative splice variants of the USH3A gene Clarin 1 (CLRN1). (PMID: 20717163) Vastinsalo H. … Sankila E.M. (Eur. J. Hum. Genet. 2011) 3 4 64
  5. CLRN1 mutations cause nonsyndromic retinitis pigmentosa. (PMID: 21310491) Khan M.I. … den Hollander A.I. (Ophthalmology 2011) 3 4 64

Products for CLRN1 Gene

Sources for CLRN1 Gene

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